Research workbench
Crystal structure of capf with inhibitor 3-isopropenyl-tropolone
Analyse Crystal structure of capf with inhibitor 3-isopropenyl-tropolone in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4YRD
- Type
- protein
- Length
- 687 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Capsular polysaccharide synthesis enzyme CAP5F
- UniProt
- Q99X63
- Ligands
- 3IT, ZN
- Pockets
- 12 · best druggability 0.60
Structure
x-ray diffraction · 2 distinct chains · 28% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Capsular polysaccharide synthesis enzyme CAP5F | protein | 341 | 28% helix, 32% strand | Q99X63 |
| B | Capsular polysaccharide synthesis enzyme CAP5F | protein | 346 | 28% helix, 32% strand | Q99X63 |
Ligands and binding sites
- 3IT · 2-hydroxy-3-(prop-1-en-2-yl)cyclohepta-2,4,6-trien-1-one · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 375 | 0.60 | 0.76 | 42 | empty |
| 2 | 230 | 0.58 | 0.79 | 24 | 3IT |
| 3 | 304 | 0.57 | 0.77 | 29 | empty |
| 4 | 240 | 0.56 | 0.78 | 27 | 3IT |
| 5 | 248 | 0.54 | 0.77 | 38 | empty |
Interfaces
1 interface between chains.
- A–B · 3477 Ų buried · 48 hydrogen bonds · protein-protein
Compared structures
- 4YRD · Crystal structure of CapF with inhibitor 3-isopropenyl-tropolone · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q99X63
- Elsewhere: RCSB PDB 4YRD · PDBe 4YRD · UniProt Q99X63
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